#4090 breaks support for Apple Silicon for formats that don't need TurboJPEG

[petebankhead]

Hi,

#4090 seems to break the use of

ImageReader reader = new ImageReader();

on Apple Silicon - even for formats that otherwise worked without problem (e.g. CMU-1.svs, LuCa tiff images).

The issue seems to be that the try/catch block doesn't handle the RuntimeException thrown whenever it is not possible to load TurboJPEG:

bioformats/components/formats-api/src/loci/formats/ImageReader.java

Lines 134 to 139 in e484e1f

	try {
	reader = c[i].newInstance();
	reader.setMetadataOptions(opt);
	}
	catch (IllegalAccessException exc) { }
	catch (InstantiationException exc) { }

The workaround is to pass a ClassList that has been already been checked to exclude classes that can't be instantiated, e.g. using

        private static ClassList<IFormatReader> getDefaultClassList() {
		ClassList<IFormatReader> classes = new ClassList<>(IFormatReader.class);
		for (var cls : ImageReader.getDefaultReaderClasses().getClasses()) {
			try {
				var instance = cls.getConstructor().newInstance();
				if (instance != null)
					classes.addClass(cls);
			} catch (Throwable t) {
				logger.debug("Cannot instantiate reader class " + cls.getName() + ": " + t.getMessage());
			}
		}
		return classes;
	}

...

ImageReader reader = new ImageReader(getDefaultClassList());

Adding code like this should be enough for us to be able to include 7.0.1 in QuPath - but since Bio-Formats is the now only dependency we have without Apple Silicon support, it would be even better if #3756 and #3858 could be addressed :) The QuPath Apple Silicon builds are now faster and more reliable on M1/M2 Macs (due in part to some OpenCV changes), so will be recommended with the caveat that most .czi images won't work.

[dgault]

Thanks @petebankhead for raising this issue, we will look at resolving this for the next release.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/bioformats-7-0-1-apple-arm-processor-regression/88713/2

[CGDogan]

For QuPath, you can remove the need for Rosetta by simply following the steps in #4042 or just copying the binary. Once you compile it with the steps I've given on any Mac computer or copy my binary, all you need to do is to unzip the bioformats-package.jar, copy the turbojpeg binary in the correct new folder, then rezip it (you need a zip tool, java's jar tool won't work) Needless to say, you would then need to distribute the turbojpeg source code to comply with GPL. I use this without problems on my Apple Silicon. I'm sure QuPath users would find it useful meanwhile.

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/files-not-opening-on-macbook-illegalstateexception/89115/6